We've known for a long time that our guts – particularly the intestines – are packed full of bacteria. These bacteria live in symbiosis with us, helping break down and digest food, forming vessels to help ferry vitamins throughout our systems, and more. In symbiotic exchange, we allow them to live.
It's only in the last few years that we've really dug into the study of the gut microbiome, trying to trace its larger effects throughout the body. The commoditization of this knowledge has led to the proliferation of probiotics as foods and supplements, but it's still very much an area of study.
To give you an idea of how important the gut biome is, research indicates that dysfunctional gut flora are linked to insulin resistance, obesity, and colorectal cancer. There's even emerging research that indicates dysfunctional microflora may even be the cause of dementia. It has exceedingly wide reach throughout the body, and it's an extremely complex machine that we just don't yet understand enough to modify with any level of consistency.
All that said, we do know some things that impact your gut flora: the foods you eat. Probiotics are a big one; they're packed full of healthy bacteria that supplement the bacteria already present. Prebiotics are a "new hotness" in the same vein, though it's really just a fancy buzzword for the food the bacteria in your gut eats, which is fiber.
On the other hand, food you eat can be detrimental to your gut biome as well. Food that feeds the wrong kinds of bacteria, or that kills some of the beneficial bacteria, or that generally just drives your system out of balance can be the cause of both short- and long-term harm. So what foods qualify, and what should you avoid?
Alcohol
It should come as no surprise that alcohol is bad for your body. After all, the entire point of alcohol is that it's mildly toxic in a way that induces some pleasant sensations. Alcohol is often used to sterilize everything from work counters to wounds, and it does that by killing the microbes present. Studies have shown that alcoholics are much more likely to experience dysbiosis – the dysfunction of the gut flora – than healthy people.
Interestingly, red wine in particular is actually beneficial to the gut biome. In another study, gut flora was tested in individuals who were then tasked with consuming red wine, non-alcoholic red win, or gin each day for three weeks. Tests showed that gin reduced healthy bacteria, but red wine helped out the healthy bacteria while suppressing the bad.
Red Meat
A diet high in red meat has a few potential ways it can hurt you over time.
For one thing, studies comparing people who have a primarily plant protein diet versus those who consume more red meat find that the meat eaters tend to have higher levels of inflammation and worse gut health. Red meat also raises your body's level of trimethylamine N-oxide, or TMAO, which is linked to a higher risk of heart attack or stroke.
For another thing, there's some fears over antibiotics in meat we consume. While the vast majority of antibiotics fed to cattle and other animals are long processed, broken down, and removed by the time the animal is slaughtered, some traces may remain. This fear, at least, can be alleviated by sourcing meat ethically.
Fried Foods
Anything you fry up in oil is going to be inherently unhealthy. Fried foods are a staple of the modern American diet, though, so it can be difficult to avoid them.
When it comes to the gut bacteria, fried foods don't do much good. In fact, the greasy, fatty foods you fry up and eat tend to feed the more harmful kinds of bacteria, while providing no sustenance to the beneficial bacteria in our guts. Not to mention all the other potential side effects, like gas, cramping, and diarrhea.
Sugar
Your body needs some kind of sugar to survive. Sugar is the way energy is transferred and processed throughout our bodies. That said, there are good sugars and there are bad sugars. Good sugars tend to come from plants and fruit, while bad sugars are the more processed white sugars and the high fructose syrups and other additives we find in all of our processed foods these days.
Sugar is also somewhat addictive. Trying to cut out sugar can be a daunting prospect, both because it's in everything and because of the cravings you'll experience. The best option is to replace sugary foods with healthy fats that fill you up and minimize cravings.
Emulsifiers
The process of emulsion is used all around you, but you may not know what it is. An emulsion is a essentially a mixture of two liquids, one finely suspended in the other. An emulsion is the processed used to make a variety of cosmetics, but it's also used broadly in food. The most common emulsion is mayonnaise, an emulsion of oil and egg.
An emulsion is typically made by rapidly mixing two ingredients, adding one gradually to the mix so it is dispersed quickly. The emulsion is then used. However, if you let it sit for too long, the ingredients will separate out. You can see this with salad dressings, for example, where oil and vinegar separate.
In order to stabilize the emulsion, another ingredient, called an emulsifier, is used. This helps prevent the emulsion from separating and making the mixture less pleasant to consume.
Unfortunately, emulsifiers can also be damaging to your gut biome. If you want to cut them out, look for ingredients like egg/soy lecithin, mono/diclycerides, polysorbates, carrageenan, and guar gum.
Gluten
Gluten might sound like a buzzword because of modern marketing, but it's actually a type of plant protein primarily found in cereal grains, like wheat, rye, and barley. The protein acts as the "glue" and gives flour its unique ability to turn into elastic dough, which in turn creates fluffy bread.
The primary disease that interacts with gluten is celiac disease, which is an autoimmune disease that causes intense discomfort and pain when consuming gluten. However, while celiac is not a very prolific disease, many people are finding that they have at least some level of sensitivity to gluten. It may only manifest itself in the form of gas and occasional discomfort, or it may be worse.
Studies are starting to show that gluten can also be a contributing factor to things like insulin resistance, inflammation, and obesity. It makes sense, then, that it fuels the wrong kind of gut bacteria.
Artificial Sweeteners
If you're cutting sugar out of your diet for health reasons, you may be tempted to replace sugary foods with other sweet foods, just the "diet" kinds with artificial sweeteners taking the place of sugar. Ingredients like stevia, aspartame, and saccharin are all universally pretty bad for you too. They just aren't bad in the same way as sugar.
This is a pretty new area of study, all things considered. It's only been in the last few decades where we've truly buckled down on the knowledge that sugar is bad for us, and have started using sugar replacements. It will likely be a few more decades before we fully understand all the ways in which those replacements are bad as well.
Dairy
There's some evidence to suggest that dairy can be pretty bad for your gut flora. Some experiments have shown that it can at the very least cause some pretty dramatic changes in a matter of days. There are two possible reasons for this.
The first is that, unlike meat, milk can carry more antibiotics from an animal. Antibiotics don't get through meat very quickly, and are mostly broken down by the time they do. Milk is a faster process and carries more with it. This is why, among other things, cheese can taste different when made with milk harvested in the spring versus in the fall. Antibiotics aren't a common problem with dairy these days, since FDA regulations limit what can be used on lactating animals, but it's still a potential issue.
The other issue is that one of the primary ingredients in milk is lactose, and lactose is a kind of sugar. We've already mentioned the issues with sugar up above. Some small amount of lactose is generally fine, unless you're lactose intolerant, but consuming a large amount of dairy every day can potentially be an issue.
Farm-Raised Fish
Fish is one kind of food animal that is still raised in largely inhumane conditions, with factory fishing accounting for a lot of issues with environmental and chemical contaminations. Farm-raised fish are packed tight in their enclosures and are dosed up with drugs to keep them healthy, otherwise a single disease could wipe out immense amounts of fish.
Farm-raised fish also frequently have high levels of mercury accumulated in their bodies. Consuming that mercury can then lead to some level of toxicity and poisoning, which is obviously dangerous to more than just your gut biome. Always strive for free-range protein sources whenever possible, be it fish, eggs, meat, or anything else.
A Lack of Variety
Finally, this last one isn't so much a food as it is all foods. If you eat the same thing every day, day after day, you end up with a lack of diversity in your gut flora. New strains don't develop, so if antibiotics or an illness wipe them out, you end up having to start from scratch rather than from a resilient population. 
While the food list above means you're going to be on a somewhat restrictive diet if you want to keep your gut healthy, you still want to look for ways to change up your food. And hey, even if you aren't doing it for your health, do it for the enjoyment of food in the first place.
A Note on GMOs
GMOs, or Genetically Modified Organisms, are a modern health fear for millions of people. Fortunately, you can put those fears to rest. "Genetic modification" is just a scientific phrase for selective breeding. A dog is a genetically modified organism, a modification of the wolf. Virtually all fruits and vegetables you eat have been genetically modified via selective breeding over the course of centuries to become larger, sweeter, and in some cases more edible. Heck, look at what watermelons used to look like.
Modern GMO fears typically tie back to something like glyphosate, like what's mentioned in this article. Glyphosate is a pesticide, and yes, it's bad for you to eat. Just like any poison, don't eat it! When people tell you that GMOs are bad and cite the glyphosate, that just means they aren't properly cleaning their vegetables before eating them. Wash your vegetables so you remove any contaminants on them, friends!
Remember that without genetic modifications, many of our most prominent crops, including most vegetables, wouldn't be nearly as productive. Food would be much less readily available. In fact, genetic modification of food has likely saved literal billions of lives over the last few centuries. Genetic modification isn't bad, eating pesticides is bad. Thankfully, you can have one without the other.
At the end of the day, what you should generally take away from this post is that heavily processed, sugar-infused, factory-farmed foods are likely to be at least somewhat bad for you. Eating a diet of a robust range of health – cleaned – vegetables, lean protein and plant protein, and fruit is going to be much better all around. And, of course, exercise and sleep help keep you healthy as well, and that includes your gut.
